Jim Procter [Wed, 7 Jan 2015 17:17:12 +0000 (17:17 +0000)]
JAL-1483 making type visible also adds it to registry
Jim Procter [Mon, 22 Dec 2014 16:16:17 +0000 (16:16 +0000)]
Merge: 497958b 68dcaa7
(fake synthesised by jbp)
Merge branch 'develop' into JAL-1483_29dev
Conflicts:
src/jalview/api/AlignmentViewPanel.java
src/jalview/appletgui/SeqPanel.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/SeqPanel.java
Jim Procter [Fri, 14 Nov 2014 12:16:32 +0000 (12:16 +0000)]
Merge branch 'develop' into JAL-1483_featureBasedTreeCalc
Conflicts:
src/jalview/api/AlignViewportI.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/ws/AWSThread.java
Jim Procter [Thu, 13 Nov 2014 16:46:06 +0000 (16:46 +0000)]
Merge branch 'features/JAL-1469_svg-output-for-figure-export' into develop
Conflicts:
.classpath
.gitignore
src/jalview/gui/AlignmentPanel.java
src/jalview/jbgui/GAlignFrame.java
Jim Procter [Thu, 13 Nov 2014 16:34:59 +0000 (16:34 +0000)]
JAL-1469 added jfreesvg to desktop dependencies
gmungoc [Thu, 13 Nov 2014 16:15:54 +0000 (16:15 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 13 Nov 2014 16:15:23 +0000 (16:15 +0000)]
merge
gmungoc [Thu, 13 Nov 2014 12:40:33 +0000 (12:40 +0000)]
JAL-1528 new Preference CHIMERA_PATH (Preferences | Structure)
gmungoc [Thu, 13 Nov 2014 11:15:42 +0000 (11:15 +0000)]
JAL-1528 Chimera tidy errors, focus after align, close option
Charles Ofoegbu [Wed, 12 Nov 2014 20:07:58 +0000 (20:07 +0000)]
house-keeping
Charles Ofoegbu [Wed, 12 Nov 2014 17:54:32 +0000 (17:54 +0000)]
Added support for SVG Export
gmungoc [Wed, 12 Nov 2014 16:55:00 +0000 (16:55 +0000)]
JAL-1528 bug fixes and adjustments to Chimera interface
Jim Procter [Wed, 12 Nov 2014 15:22:42 +0000 (15:22 +0000)]
Merge branch 'features/JAL-1541_BioJsMSAViewer-export-option' into develop
Jim Procter [Wed, 12 Nov 2014 15:22:34 +0000 (15:22 +0000)]
JAL-1541 exclude all unnecessary jalview.io classes from applet build
Jim Procter [Wed, 12 Nov 2014 15:20:41 +0000 (15:20 +0000)]
Merge branch 'features/JAL-1541_BioJsMSAViewer-export-option' into develop
Jim Procter [Wed, 12 Nov 2014 15:19:19 +0000 (15:19 +0000)]
Merge branch 'develop' into features/JAL-1541_BioJsMSAViewer-export-option
Jim Procter [Wed, 12 Nov 2014 14:56:03 +0000 (14:56 +0000)]
Merge branch 'features/typed_annotations_calcId' into develop
Jim Procter [Wed, 12 Nov 2014 14:55:45 +0000 (14:55 +0000)]
JAL-974 fix class contamination for jalviewLite build
gmungoc [Wed, 12 Nov 2014 14:30:46 +0000 (14:30 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Jim Procter [Wed, 12 Nov 2014 12:41:52 +0000 (12:41 +0000)]
Merge branch 'features/typed_annotations_calcId' into develop
Jim Procter [Wed, 12 Nov 2014 12:40:43 +0000 (12:40 +0000)]
javadoc
Jim Procter [Wed, 12 Nov 2014 12:40:24 +0000 (12:40 +0000)]
JAL-674 use the getMapping/transfer to transfer annotation when creating a mapping to a sequence
Jim Procter [Wed, 12 Nov 2014 12:39:50 +0000 (12:39 +0000)]
JAL-674 patch broken getMapping function
Jim Procter [Wed, 12 Nov 2014 12:39:05 +0000 (12:39 +0000)]
JAL-674 switch from .transfer to .liftOver for transfer of annotation
Jim Procter [Wed, 12 Nov 2014 12:37:12 +0000 (12:37 +0000)]
JAL-674 note about broken .transfer method (expect this to disappear in future!)
Jim Procter [Wed, 12 Nov 2014 12:36:36 +0000 (12:36 +0000)]
JAL-674 javadoc
Jim Procter [Wed, 12 Nov 2014 12:35:40 +0000 (12:35 +0000)]
JAL-674 new tests and deprecated tests for PDB mapping to sequence code
Charles Ofoegbu [Wed, 12 Nov 2014 12:19:55 +0000 (12:19 +0000)]
Excluded HtmlFile.java dependencies from AppletFomatAdapter
Jim Procter [Wed, 12 Nov 2014 10:39:08 +0000 (10:39 +0000)]
JAL-1541 added Jsoup to the InstallAnywhere config
Jim Procter [Wed, 12 Nov 2014 10:29:16 +0000 (10:29 +0000)]
JAL-1541 added Jsoup to the InstallAnywhere config
Jim Procter [Wed, 12 Nov 2014 10:28:25 +0000 (10:28 +0000)]
JAL-1541 added Jsoup to the InstallAnywhere config
Charles Ofoegbu [Wed, 12 Nov 2014 10:23:25 +0000 (10:23 +0000)]
mearge with develop
Jim Procter [Wed, 12 Nov 2014 10:15:59 +0000 (10:15 +0000)]
JAL-1541 added Jsoup to the InstallAnywhere config
Charles Ofoegbu [Wed, 12 Nov 2014 09:30:02 +0000 (09:30 +0000)]
Modified biojs exporter/importer to preserve SequenceFeatures during a write/read operation
gmungoc [Tue, 11 Nov 2014 09:20:40 +0000 (09:20 +0000)]
JAL-1527 opening a project saved with JMol should use JMol (disregard
viewer preference).
Charles Ofoegbu [Fri, 7 Nov 2014 12:08:22 +0000 (12:08 +0000)]
Updated BioJsTemplate to not show the menu by default and implemented a toggle button for the menu, also the LableId was disabled by default
Charles Ofoegbu [Fri, 7 Nov 2014 09:46:37 +0000 (09:46 +0000)]
Modified BioJsHTMLOutput.java to clean up and close used resources properly
Charles Ofoegbu [Fri, 7 Nov 2014 09:31:09 +0000 (09:31 +0000)]
Modified BioJsHTMLOutput.java to use class loader while loading BioJsTemplate file
Charles Ofoegbu [Thu, 6 Nov 2014 18:19:53 +0000 (18:19 +0000)]
Changes from JAL-1541 patch
Charles Ofoegbu [Thu, 6 Nov 2014 17:47:38 +0000 (17:47 +0000)]
Updated BioJs Html to be capable of launching jalivew
Jim Procter [Thu, 6 Nov 2014 17:18:44 +0000 (17:18 +0000)]
Merge branch 'features/JAL-1152annotationSorting' into features/typed_annotations_calcId
Jim Procter [Thu, 6 Nov 2014 16:33:25 +0000 (16:33 +0000)]
Merge branch 'features/JAL-1541_BioJsMSAViewer-export-option' into develop
gmungoc [Thu, 6 Nov 2014 14:33:26 +0000 (14:33 +0000)]
JAL-1152 use a proper RadioButton not a faked one
gmungoc [Wed, 5 Nov 2014 16:04:10 +0000 (16:04 +0000)]
JAL-674 Prefences tweaks incl help documentation for Structure tab
gmungoc [Wed, 5 Nov 2014 12:21:23 +0000 (12:21 +0000)]
JAL-1152 new Structure tab on Preferences for SS derivation / annotation
gmungoc [Tue, 4 Nov 2014 09:37:50 +0000 (09:37 +0000)]
JAL-1152 help updates for Preferences
gmungoc [Tue, 4 Nov 2014 09:10:14 +0000 (09:10 +0000)]
JAL-1152 annotation sort algorithm optimisation
Jim Procter [Tue, 4 Nov 2014 08:19:19 +0000 (08:19 +0000)]
JAL-1213 normalise sequence extracted from Jmol in same way as MCview
Jim Procter [Tue, 4 Nov 2014 08:11:59 +0000 (08:11 +0000)]
JAL-1213 test to ensure JMol extracted sequences are same as MCView
gmungoc [Mon, 3 Nov 2014 16:59:26 +0000 (16:59 +0000)]
Merge branch 'features/JAL-1152annotationSorting' of https://source.jalview.org/git/jalview.git into features/JAL-1152annotationSorting
gmungoc [Mon, 3 Nov 2014 16:59:04 +0000 (16:59 +0000)]
JAL-1152 annotation sorting preferences and help documentation
Jim Procter [Mon, 3 Nov 2014 16:13:35 +0000 (16:13 +0000)]
Merge branch 'develop' into features/JAL-1152annotationSorting
Jim Procter [Mon, 3 Nov 2014 16:12:44 +0000 (16:12 +0000)]
Merge branch 'bug/JAL-1250_redundance-removal' into develop
Jim Procter [Mon, 3 Nov 2014 16:02:18 +0000 (16:02 +0000)]
Merge branch 'develop' into features/JAL-1152annotationSorting
Jim Procter [Mon, 3 Nov 2014 16:01:56 +0000 (16:01 +0000)]
Merge branch 'features/ssFromPDBEntry' into develop
Jim Procter [Mon, 3 Nov 2014 15:51:04 +0000 (15:51 +0000)]
JAL-795 JAL-674 tweaked logic to avoid black annotation shading and hard-wire secondary structure colours when no custom colours available
Jim Procter [Mon, 3 Nov 2014 13:02:39 +0000 (13:02 +0000)]
fix for JAL-1579 create threshold object for annotation rows that match shading pattern but do not have threshold objects as yet (nb - side effect is that cancel leaves old threshold lines on these annotation)
Jim Procter [Mon, 3 Nov 2014 10:10:09 +0000 (10:10 +0000)]
JAL-1578 test property accessors/copy constructor
Jim Procter [Mon, 3 Nov 2014 10:09:08 +0000 (10:09 +0000)]
JAL-1578 JAL-674 store/restore alignment annotation properties in Jalview 2.8.2 project (allows the Annotated PDB file import/export to project/import test to pass)
Jim Procter [Mon, 3 Nov 2014 10:04:09 +0000 (10:04 +0000)]
JAL-1578 formatting and imports
Jim Procter [Mon, 3 Nov 2014 10:03:22 +0000 (10:03 +0000)]
JAL-674 peptide structure input so test is not dependent on network
Jim Procter [Mon, 3 Nov 2014 10:02:27 +0000 (10:02 +0000)]
JAL-1551 formatting
Jim Procter [Mon, 3 Nov 2014 10:01:43 +0000 (10:01 +0000)]
JAL-674 JAL-961 JAL-1578 accessors and copy constructor for annotation row properties
Jim Procter [Mon, 3 Nov 2014 09:58:29 +0000 (09:58 +0000)]
javadoc
gmungoc [Fri, 31 Oct 2014 16:43:46 +0000 (16:43 +0000)]
JAL-1152 bug fix for 'no sort' case + tests for autocalc placement
gmungoc [Fri, 31 Oct 2014 16:18:33 +0000 (16:18 +0000)]
JAL-1152 menu tweaks plus new option to put Autocalc at top or below.
Jim Procter [Fri, 31 Oct 2014 16:14:27 +0000 (16:14 +0000)]
JAL-674 JAL-961 pass row reference to handler to check calcId and any specific properties (e.g. originating PDB ID for the row data)
Jim Procter [Fri, 31 Oct 2014 16:11:45 +0000 (16:11 +0000)]
JAL-674 JAL-961 properties to stash additional information for an alignment annotation row
Charles Ofoegbu [Fri, 31 Oct 2014 12:57:09 +0000 (12:57 +0000)]
added jsoup lib to class path
Charles Ofoegbu [Fri, 31 Oct 2014 09:56:45 +0000 (09:56 +0000)]
JAL-1541 upadated BioJs emmitter to store alignment data as json
Jim Procter [Thu, 30 Oct 2014 17:05:36 +0000 (17:05 +0000)]
Merge branch 'develop' into features/ssFromPDBEntry
Jim Procter [Thu, 30 Oct 2014 16:53:20 +0000 (16:53 +0000)]
JAL-674 hang on to sequences created by secondary parsiing process to manage transfer of annotation
Jim Procter [Thu, 30 Oct 2014 16:51:10 +0000 (16:51 +0000)]
JAL-674 count number of annotation transferred in test
gmungoc [Thu, 30 Oct 2014 16:29:01 +0000 (16:29 +0000)]
JAL-1152 with sticky annotation sort order that updates as sequences are
moved up or down
Jim Procter [Thu, 30 Oct 2014 15:51:54 +0000 (15:51 +0000)]
JAL-674 propagate annotation onto mapped sequence and its dataset sequence
Jim Procter [Thu, 30 Oct 2014 15:50:30 +0000 (15:50 +0000)]
JAL-674 register PDB IDs when ever they are resolved on file IO
Jim Procter [Thu, 30 Oct 2014 15:47:07 +0000 (15:47 +0000)]
JAL-674 use PDB ID<>File registry to look up correct ID for PDB file derived annotation on a mapped sequence
Jim Procter [Thu, 30 Oct 2014 15:44:50 +0000 (15:44 +0000)]
JAL-674 return original and replacement sequences and the alignment to allow more processing if needed
Jim Procter [Thu, 30 Oct 2014 15:40:31 +0000 (15:40 +0000)]
JAL-674 helpful javadoc for remap method
Jim Procter [Thu, 30 Oct 2014 15:39:53 +0000 (15:39 +0000)]
JAL-674 flag and proxy method to distinguish setMapping calls which create a mapping for a displayed structure and those which transfer annotation
Jim Procter [Thu, 30 Oct 2014 15:30:50 +0000 (15:30 +0000)]
JAL-674 map on StructureSelectionManager to record PDB IDs extracted/assigned to PDB files
Jim Procter [Thu, 30 Oct 2014 15:26:11 +0000 (15:26 +0000)]
patch for JAL-795 - use base secondary structure colour if no colour defined on annotation row element
Jim Procter [Thu, 30 Oct 2014 15:24:00 +0000 (15:24 +0000)]
JAL-674 patch test to verify presence of annotation on the sequence associated with the PDB file
Jim Procter [Thu, 30 Oct 2014 15:21:31 +0000 (15:21 +0000)]
JAL-1551 format and tidy
gmungoc [Thu, 30 Oct 2014 14:18:42 +0000 (14:18 +0000)]
JAL-1152 prototype of new Annotations menu with sort options
Charles Ofoegbu [Thu, 30 Oct 2014 12:27:40 +0000 (12:27 +0000)]
JAL-353 updated patch for undo successive remove redundant sequence
Charles Ofoegbu [Thu, 30 Oct 2014 12:18:10 +0000 (12:18 +0000)]
Modified biojs template file
Charles Ofoegbu [Thu, 30 Oct 2014 10:35:04 +0000 (10:35 +0000)]
JAL-1541 BioJs MSA Viewer export option implementation
Charles Ofoegbu [Wed, 29 Oct 2014 19:05:37 +0000 (19:05 +0000)]
JAL-353 updated patch for undo successive remove redundant sequences
Jim Procter [Wed, 29 Oct 2014 10:47:13 +0000 (10:47 +0000)]
JAL-1264 JAL-674 test to exercise the AlignmentAnnotation.remap method via
the jalview.structure.StructureMapping.transfer method
Jim Procter [Wed, 29 Oct 2014 10:44:33 +0000 (10:44 +0000)]
JAL-1264 JAL-674 method to copy annotation on structure positions to associated sequence positions
Jim Procter [Wed, 29 Oct 2014 10:41:32 +0000 (10:41 +0000)]
JAL-674 JAL-1264 remap method to allow annotation positions to be updated from simple int-pair arrays (like those used in the StructureManager mappings)
gmungoc [Tue, 28 Oct 2014 15:52:53 +0000 (15:52 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Tue, 28 Oct 2014 15:51:46 +0000 (15:51 +0000)]
JAL-1264 refactor to add menu options to _both_ sequence and selection
pop-ups, plus unit tests.
Charles Ofoegbu [Tue, 28 Oct 2014 11:03:09 +0000 (11:03 +0000)]
2_8_2_Branch merge
Charles Ofoegbu [Tue, 28 Oct 2014 10:35:44 +0000 (10:35 +0000)]
JAL-353 undo for successive removal of redundant sequence - bugfix
Charles Ofoegbu [Tue, 28 Oct 2014 10:32:23 +0000 (10:32 +0000)]
JAL-1250 Redundancy removal bug fix for Applet version
Jim Procter [Mon, 27 Oct 2014 13:40:20 +0000 (13:40 +0000)]
Merge branch 'develop' into Release_2_8_2_Branch
Jim Procter [Mon, 27 Oct 2014 13:39:38 +0000 (13:39 +0000)]
Merge branch 'Release_2_8_2_Branch' into merge_r282_dev
normalised HTML messages and line endings for JAL-1420 JAL-1428 JAL-1355
(darolmar commits)
Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties
Charles Ofoegbu [Mon, 27 Oct 2014 13:06:19 +0000 (13:06 +0000)]
Updated RedundancyPanel.java to referesh the tree view when reduncancy is applied/unapplied
git://source.jalview.org / jalview.git / log